Starting phenix.real_space_refine on Wed Mar 4 13:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtb_27695/03_2026/8dtb_27695.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 9053 2.51 5 N 2219 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13724 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 257 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 9, 'TRANS': 427} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 14, 'TRP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 9, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 5, 'ASP:plan': 13, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3360 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 426} Chain breaks: 4 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 18, 'ASP:plan': 14, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 149 Chain: "J" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 9, 'TRANS': 423} Chain breaks: 5 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'TRP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 10, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 13724 At special positions: 0 Unit cell: (100.58, 140.17, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 12 15.00 O 2352 8.00 N 2219 7.00 C 9053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 21 " distance=2.01 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 32 " distance=2.06 Simple disulfide: pdb=" SG CYS G4876 " - pdb=" SG CYS G4882 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Simple disulfide: pdb=" SG CYS J4876 " - pdb=" SG CYS J4882 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 441.8 milliseconds 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 4 sheets defined 76.5% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'G' and resid 4209 through 4225 Processing helix chain 'G' and resid 4229 through 4252 Processing helix chain 'G' and resid 4324 through 4342 Processing helix chain 'G' and resid 4542 through 4558 removed outlier: 4.266A pdb=" N VAL G4546 " --> pdb=" O GLY G4542 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN G4547 " --> pdb=" O GLU G4543 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN G4558 " --> pdb=" O TYR G4554 " (cutoff:3.500A) Processing helix chain 'G' and resid 4558 through 4578 Processing helix chain 'G' and resid 4639 through 4665 removed outlier: 3.683A pdb=" N LEU G4648 " --> pdb=" O TRP G4644 " (cutoff:3.500A) Processing helix chain 'G' and resid 4665 through 4683 Processing helix chain 'G' and resid 4685 through 4690 Processing helix chain 'G' and resid 4696 through 4702 Processing helix chain 'G' and resid 4703 through 4706 removed outlier: 3.603A pdb=" N LEU G4706 " --> pdb=" O ARG G4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4703 through 4706' Processing helix chain 'G' and resid 4719 through 4728 Processing helix chain 'G' and resid 4733 through 4742 Processing helix chain 'G' and resid 4767 through 4771 Processing helix chain 'G' and resid 4772 through 4786 Processing helix chain 'G' and resid 4786 through 4806 removed outlier: 3.826A pdb=" N HIS G4803 " --> pdb=" O SER G4799 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR G4804 " --> pdb=" O LEU G4800 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN G4805 " --> pdb=" O LEU G4801 " (cutoff:3.500A) Processing helix chain 'G' and resid 4807 through 4813 Processing helix chain 'G' and resid 4814 through 4820 removed outlier: 3.628A pdb=" N MET G4818 " --> pdb=" O LEU G4814 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) Processing helix chain 'G' and resid 4820 through 4833 removed outlier: 3.875A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN G4833 " --> pdb=" O SER G4829 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 Processing helix chain 'G' and resid 4878 through 4889 Processing helix chain 'G' and resid 4889 through 4894 removed outlier: 4.240A pdb=" N GLY G4894 " --> pdb=" O GLY G4890 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4926 Processing helix chain 'G' and resid 4927 through 4956 Processing helix chain 'A' and resid 4209 through 4224 removed outlier: 3.920A pdb=" N SER A4213 " --> pdb=" O GLN A4209 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4251 removed outlier: 4.386A pdb=" N PHE A4243 " --> pdb=" O GLU A4239 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A4244 " --> pdb=" O ASP A4240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A4245 " --> pdb=" O THR A4241 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A4246 " --> pdb=" O ILE A4242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4324 through 4342 Processing helix chain 'A' and resid 4552 through 4558 removed outlier: 3.705A pdb=" N ARG A4557 " --> pdb=" O ASN A4553 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4577 Processing helix chain 'A' and resid 4638 through 4665 removed outlier: 3.903A pdb=" N ASN A4662 " --> pdb=" O ILE A4658 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A4663 " --> pdb=" O ILE A4659 " (cutoff:3.500A) Processing helix chain 'A' and resid 4665 through 4684 Processing helix chain 'A' and resid 4696 through 4702 removed outlier: 3.551A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4707 removed outlier: 3.890A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4702 through 4707' Processing helix chain 'A' and resid 4720 through 4728 removed outlier: 3.991A pdb=" N VAL A4724 " --> pdb=" O VAL A4720 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4741 Processing helix chain 'A' and resid 4772 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.785A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 3.781A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 4.038A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4878 through 4894 removed outlier: 4.113A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A4894 " --> pdb=" O GLY A4890 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 removed outlier: 3.729A pdb=" N ASP A4899 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A4900 " --> pdb=" O ILE A4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4896 through 4900' Processing helix chain 'A' and resid 4909 through 4925 Processing helix chain 'A' and resid 4927 through 4957 removed outlier: 3.769A pdb=" N GLN A4947 " --> pdb=" O LEU A4943 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A4948 " --> pdb=" O ARG A4944 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.917A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4209 through 4224 Processing helix chain 'D' and resid 4229 through 4252 removed outlier: 3.527A pdb=" N PHE D4243 " --> pdb=" O GLU D4239 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D4246 " --> pdb=" O ILE D4242 " (cutoff:3.500A) Processing helix chain 'D' and resid 4324 through 4341 Processing helix chain 'D' and resid 4542 through 4558 removed outlier: 3.894A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4636 through 4638 No H-bonds generated for 'chain 'D' and resid 4636 through 4638' Processing helix chain 'D' and resid 4639 through 4665 removed outlier: 4.051A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) Processing helix chain 'D' and resid 4665 through 4684 Processing helix chain 'D' and resid 4696 through 4702 removed outlier: 3.796A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4706 removed outlier: 3.860A pdb=" N LEU D4706 " --> pdb=" O ARG D4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4703 through 4706' Processing helix chain 'D' and resid 4719 through 4728 Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.926A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN D4805 " --> pdb=" O LEU D4801 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 removed outlier: 3.932A pdb=" N PHE D4809 " --> pdb=" O ASN D4806 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D4810 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D4811 " --> pdb=" O PHE D4808 " (cutoff:3.500A) Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.059A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.856A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4858 removed outlier: 3.567A pdb=" N VAL D4854 " --> pdb=" O LEU D4850 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4889 Processing helix chain 'D' and resid 4889 through 4894 removed outlier: 4.295A pdb=" N GLY D4894 " --> pdb=" O GLY D4890 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4925 Processing helix chain 'D' and resid 4927 through 4956 removed outlier: 3.746A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D4939 " --> pdb=" O LEU D4935 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 Processing helix chain 'J' and resid 4209 through 4224 Processing helix chain 'J' and resid 4229 through 4252 removed outlier: 3.682A pdb=" N PHE J4243 " --> pdb=" O GLU J4239 " (cutoff:3.500A) Processing helix chain 'J' and resid 4324 through 4341 Processing helix chain 'J' and resid 4542 through 4558 removed outlier: 3.555A pdb=" N ASN J4558 " --> pdb=" O TYR J4554 " (cutoff:3.500A) Processing helix chain 'J' and resid 4559 through 4578 Processing helix chain 'J' and resid 4638 through 4665 removed outlier: 3.523A pdb=" N ALA J4642 " --> pdb=" O TYR J4638 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP J4644 " --> pdb=" O GLU J4640 " (cutoff:3.500A) Processing helix chain 'J' and resid 4665 through 4684 removed outlier: 3.543A pdb=" N VAL J4669 " --> pdb=" O LYS J4665 " (cutoff:3.500A) Processing helix chain 'J' and resid 4697 through 4703 Processing helix chain 'J' and resid 4704 through 4708 Processing helix chain 'J' and resid 4719 through 4728 removed outlier: 3.713A pdb=" N LYS J4723 " --> pdb=" O PHE J4719 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS J4728 " --> pdb=" O VAL J4724 " (cutoff:3.500A) Processing helix chain 'J' and resid 4733 through 4742 removed outlier: 3.994A pdb=" N LEU J4740 " --> pdb=" O ARG J4736 " (cutoff:3.500A) Processing helix chain 'J' and resid 4772 through 4786 Processing helix chain 'J' and resid 4786 through 4805 removed outlier: 3.948A pdb=" N HIS J4803 " --> pdb=" O SER J4799 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR J4804 " --> pdb=" O LEU J4800 " (cutoff:3.500A) Processing helix chain 'J' and resid 4806 through 4813 removed outlier: 3.550A pdb=" N PHE J4809 " --> pdb=" O ASN J4806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA J4811 " --> pdb=" O PHE J4808 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J4813 " --> pdb=" O ALA J4810 " (cutoff:3.500A) Processing helix chain 'J' and resid 4814 through 4820 removed outlier: 4.187A pdb=" N MET J4818 " --> pdb=" O LEU J4814 " (cutoff:3.500A) Processing helix chain 'J' and resid 4820 through 4833 removed outlier: 3.914A pdb=" N VAL J4830 " --> pdb=" O ILE J4826 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR J4831 " --> pdb=" O LEU J4827 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN J4833 " --> pdb=" O SER J4829 " (cutoff:3.500A) Processing helix chain 'J' and resid 4833 through 4858 Processing helix chain 'J' and resid 4878 through 4894 removed outlier: 3.992A pdb=" N VAL J4891 " --> pdb=" O MET J4887 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG J4892 " --> pdb=" O TYR J4888 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY J4894 " --> pdb=" O GLY J4890 " (cutoff:3.500A) Processing helix chain 'J' and resid 4896 through 4900 removed outlier: 3.673A pdb=" N ASP J4899 " --> pdb=" O GLY J4896 " (cutoff:3.500A) Processing helix chain 'J' and resid 4909 through 4925 Processing helix chain 'J' and resid 4927 through 4957 Processing helix chain 'J' and resid 4964 through 4969 removed outlier: 4.128A pdb=" N PHE J4968 " --> pdb=" O GLY J4964 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 4580 through 4583 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 removed outlier: 3.669A pdb=" N SER A4583 " --> pdb=" O VAL A4628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4580 through 4583 Processing sheet with id=AA4, first strand: chain 'J' and resid 4580 through 4583 929 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2480 1.33 - 1.45: 3780 1.45 - 1.57: 7644 1.57 - 1.70: 21 1.70 - 1.82: 138 Bond restraints: 14063 Sorted by residual: bond pdb=" C ILE G4932 " pdb=" O ILE G4932 " ideal model delta sigma weight residual 1.237 1.297 -0.060 1.12e-02 7.97e+03 2.89e+01 bond pdb=" N GLN A4691 " pdb=" CA GLN A4691 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.91e+01 bond pdb=" C TYR D4638 " pdb=" N MET D4639 " ideal model delta sigma weight residual 1.333 1.287 0.046 1.43e-02 4.89e+03 1.03e+01 bond pdb=" N ILE G4936 " pdb=" CA ILE G4936 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ILE G4932 " pdb=" CA ILE G4932 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.18e+00 ... (remaining 14058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18723 1.94 - 3.88: 319 3.88 - 5.83: 58 5.83 - 7.77: 7 7.77 - 9.71: 7 Bond angle restraints: 19114 Sorted by residual: angle pdb=" C CYS B 21 " pdb=" CA CYS B 21 " pdb=" CB CYS B 21 " ideal model delta sigma weight residual 111.74 102.14 9.60 1.37e+00 5.33e-01 4.91e+01 angle pdb=" N ALA D4939 " pdb=" CA ALA D4939 " pdb=" C ALA D4939 " ideal model delta sigma weight residual 111.11 117.90 -6.79 1.20e+00 6.94e-01 3.20e+01 angle pdb=" C PRO A4692 " pdb=" CA PRO A4692 " pdb=" CB PRO A4692 " ideal model delta sigma weight residual 112.64 104.57 8.07 1.43e+00 4.89e-01 3.18e+01 angle pdb=" N GLN G4933 " pdb=" CA GLN G4933 " pdb=" C GLN G4933 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" CA ILE G4931 " pdb=" C ILE G4931 " pdb=" O ILE G4931 " ideal model delta sigma weight residual 120.85 116.30 4.55 1.06e+00 8.90e-01 1.84e+01 ... (remaining 19109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6855 17.70 - 35.40: 906 35.40 - 53.11: 310 53.11 - 70.81: 45 70.81 - 88.51: 15 Dihedral angle restraints: 8131 sinusoidal: 3000 harmonic: 5131 Sorted by residual: dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS B 21 " pdb=" CB CYS B 21 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 32 " pdb=" CB CYS B 32 " ideal model delta sinusoidal sigma weight residual -86.00 -121.70 35.70 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CB CYS B 3 " pdb=" SG CYS B 3 " pdb=" SG CYS B 17 " pdb=" CB CYS B 17 " ideal model delta sinusoidal sigma weight residual -86.00 -119.45 33.45 1 1.00e+01 1.00e-02 1.59e+01 ... (remaining 8128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1952 0.061 - 0.123: 196 0.123 - 0.184: 20 0.184 - 0.245: 5 0.245 - 0.307: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CG LEU A4331 " pdb=" CB LEU A4331 " pdb=" CD1 LEU A4331 " pdb=" CD2 LEU A4331 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE D4937 " pdb=" N ILE D4937 " pdb=" C ILE D4937 " pdb=" CB ILE D4937 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA CYS B 21 " pdb=" N CYS B 21 " pdb=" C CYS B 21 " pdb=" CB CYS B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2171 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D4637 " 0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C GLY D4637 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY D4637 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR D4638 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN G4691 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.81e+00 pdb=" N PRO G4692 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO G4692 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G4692 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY G4637 " -0.013 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C GLY G4637 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY G4637 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G4638 " -0.016 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 412 2.72 - 3.26: 13920 3.26 - 3.81: 22843 3.81 - 4.35: 25952 4.35 - 4.90: 44833 Nonbonded interactions: 107960 Sorted by model distance: nonbonded pdb=" OG1 THR G4689 " pdb=" OE1 GLU G4690 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR D4687 " pdb=" O GLY D4699 " model vdw 2.203 3.040 nonbonded pdb=" O GLU J4952 " pdb=" OG1 THR J4956 " model vdw 2.215 3.040 nonbonded pdb=" O GLY A4781 " pdb=" OG1 THR A4785 " model vdw 2.225 3.040 nonbonded pdb=" O ALA J4248 " pdb=" OG SER J4252 " model vdw 2.233 3.040 ... (remaining 107955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 or (resid 4211 through 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4219 or (resid 4220 \ and (name N or name CA or name C or name O or name CB )) or resid 4221 through 4 \ 551 or (resid 4552 and (name N or name CA or name C or name O or name CB )) or r \ esid 4553 through 4690 or (resid 4691 and (name N or name CA or name C or name O \ or name CB )) or resid 4692 or resid 4696 through 4697 or (resid 4698 and (name \ N or name CA or name C or name O or name CB )) or resid 4699 through 4725 or (r \ esid 4726 through 4727 and (name N or name CA or name C or name O or name CB )) \ or resid 4728 through 4736 or (resid 4737 through 4739 and (name N or name CA or \ name C or name O or name CB )) or resid 4740 through 4742 or resid 4769 through \ 4785 or (resid 4786 and (name N or name CA or name C or name O or name CB )) or \ resid 4787 through 4965 or (resid 4966 and (name N or name CA or name C or name \ O or name CB )) or resid 4967 through 4968 or resid 5103)) selection = (chain 'D' and (resid 4208 through 4210 or (resid 4211 through 4212 and (name N \ or name CA or name C or name O or name CB )) or resid 4213 through 4223 or (resi \ d 4224 and (name N or name CA or name C or name O or name CB )) or resid 4225 th \ rough 4243 or (resid 4244 and (name N or name CA or name C or name O or name CB \ )) or resid 4245 through 4251 or resid 4323 through 4340 or (resid 4341 through \ 4342 and (name N or name CA or name C or name O or name CB )) or resid 4343 thro \ ugh 4344 or resid 4549 through 4551 or (resid 4552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4553 through 4639 or (resid 4640 and (name \ N or name CA or name C or name O or name CB )) or resid 4641 through 4679 or (re \ sid 4680 and (name N or name CA or name C or name O or name CB )) or resid 4681 \ through 4689 or (resid 4690 through 4691 and (name N or name CA or name C or nam \ e O or name CB )) or resid 4692 or resid 4696 through 4717 or (resid 4718 and (n \ ame N or name CA or name C or name O or name CB )) or resid 4719 through 4721 or \ (resid 4722 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 723 through 4725 or (resid 4726 through 4727 and (name N or name CA or name C or \ name O or name CB )) or resid 4728 through 4730 or (resid 4731 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4732 through 4733 or (resid 47 \ 34 through 4739 and (name N or name CA or name C or name O or name CB )) or resi \ d 4740 through 4742 or (resid 4769 through 4772 and (name N or name CA or name C \ or name O or name CB )) or resid 4773 through 4785 or (resid 4786 and (name N o \ r name CA or name C or name O or name CB )) or resid 4787 through 4820 or (resid \ 4821 and (name N or name CA or name C or name O or name CB )) or resid 4822 thr \ ough 4956 or (resid 4957 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4958 through 4968 or resid 5104)) selection = (chain 'G' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 or (resid 4211 through 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4243 or (resid 4244 \ and (name N or name CA or name C or name O or name CB )) or resid 4245 through 4 \ 251 or resid 4323 through 4340 or (resid 4341 through 4342 and (name N or name C \ A or name C or name O or name CB )) or resid 4343 through 4344 or resid 4549 thr \ ough 4551 or (resid 4552 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4553 through 4679 or (resid 4680 and (name N or name CA or name C or \ name O or name CB )) or resid 4681 through 4689 or (resid 4690 through 4691 and \ (name N or name CA or name C or name O or name CB )) or resid 4692 or resid 4696 \ through 4702 or (resid 4703 and (name N or name CA or name C or name O or name \ CB )) or resid 4704 through 4721 or (resid 4722 and (name N or name CA or name C \ or name O or name CB )) or resid 4723 through 4742 or (resid 4769 through 4772 \ and (name N or name CA or name C or name O or name CB )) or resid 4773 through 4 \ 820 or (resid 4821 and (name N or name CA or name C or name O or name CB )) or r \ esid 4822 through 4965 or (resid 4966 and (name N or name CA or name C or name O \ or name CB )) or resid 4967 through 5301)) selection = (chain 'J' and (resid 4208 or (resid 4209 and (name N or name CA or name C or na \ me O or name CB )) or resid 4210 through 4211 or (resid 4212 and (name N or name \ CA or name C or name O or name CB )) or resid 4213 through 4219 or (resid 4220 \ and (name N or name CA or name C or name O or name CB )) or resid 4221 through 4 \ 223 or (resid 4224 and (name N or name CA or name C or name O or name CB )) or r \ esid 4225 through 4243 or (resid 4244 and (name N or name CA or name C or name O \ or name CB )) or resid 4245 through 4251 or resid 4323 through 4340 or (resid 4 \ 341 through 4342 and (name N or name CA or name C or name O or name CB )) or res \ id 4343 through 4344 or resid 4549 through 4679 or (resid 4680 and (name N or na \ me CA or name C or name O or name CB )) or resid 4681 through 4697 or (resid 469 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 4699 through \ 4721 or (resid 4722 and (name N or name CA or name C or name O or name CB )) or \ resid 4723 through 4725 or (resid 4726 through 4727 and (name N or name CA or n \ ame C or name O or name CB )) or resid 4728 through 4736 or (resid 4737 through \ 4739 and (name N or name CA or name C or name O or name CB )) or resid 4740 thro \ ugh 4742 or (resid 4769 through 4772 and (name N or name CA or name C or name O \ or name CB )) or resid 4773 or (resid 4774 and (name N or name CA or name C or n \ ame O or name CB )) or resid 4775 through 4785 or (resid 4786 and (name N or nam \ e CA or name C or name O or name CB )) or resid 4787 through 4820 or (resid 4821 \ and (name N or name CA or name C or name O or name CB )) or resid 4822 through \ 4954 or (resid 4955 and (name N or name CA or name C or name O or name CB )) or \ resid 4956 through 4968 or resid 5105)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 14070 Z= 0.200 Angle : 0.624 9.712 19128 Z= 0.377 Chirality : 0.039 0.307 2174 Planarity : 0.004 0.070 2340 Dihedral : 18.081 88.510 4806 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 28.96 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1721 helix: 1.71 (0.15), residues: 1209 sheet: -0.30 (0.77), residues: 42 loop : -1.62 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D4679 TYR 0.016 0.001 TYR J4851 PHE 0.036 0.001 PHE J4671 TRP 0.011 0.001 TRP D4794 HIS 0.007 0.000 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00338 (14063) covalent geometry : angle 0.61896 (19114) SS BOND : bond 0.01533 ( 7) SS BOND : angle 2.86678 ( 14) hydrogen bonds : bond 0.14320 ( 929) hydrogen bonds : angle 5.12504 ( 2727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 358 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4551 PHE cc_start: 0.7247 (m-10) cc_final: 0.6752 (m-10) REVERT: G 4638 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: A 4698 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8102 (mtmm) REVERT: D 4849 TYR cc_start: 0.8475 (t80) cc_final: 0.7992 (t80) REVERT: J 4862 PHE cc_start: 0.5488 (m-10) cc_final: 0.5043 (m-80) REVERT: J 4900 GLU cc_start: 0.7742 (mp0) cc_final: 0.7455 (mp0) outliers start: 13 outliers final: 7 residues processed: 366 average time/residue: 0.1071 time to fit residues: 58.5500 Evaluate side-chains 359 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 350 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain A residue 4231 MET Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4698 LYS Chi-restraints excluded: chain J residue 4704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J4707 ASN J4836 GLN J4857 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159986 restraints weight = 17367.456| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.33 r_work: 0.3695 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14070 Z= 0.128 Angle : 0.481 5.991 19128 Z= 0.263 Chirality : 0.036 0.133 2174 Planarity : 0.004 0.059 2340 Dihedral : 9.247 89.415 2047 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.79 % Allowed : 24.49 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1721 helix: 1.87 (0.15), residues: 1206 sheet: -0.16 (0.81), residues: 42 loop : -1.62 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D4679 TYR 0.013 0.001 TYR D4629 PHE 0.023 0.001 PHE J4671 TRP 0.009 0.001 TRP G4778 HIS 0.006 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00274 (14063) covalent geometry : angle 0.47999 (19114) SS BOND : bond 0.00141 ( 7) SS BOND : angle 0.96749 ( 14) hydrogen bonds : bond 0.04197 ( 929) hydrogen bonds : angle 4.04275 ( 2727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4638 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5479 (p90) REVERT: G 4740 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (tp) REVERT: G 4824 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: G 4948 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 4215 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7771 (mmt180) REVERT: A 4679 ARG cc_start: 0.6982 (mmm160) cc_final: 0.6592 (mmt-90) REVERT: D 4580 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: D 4676 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 4796 MET cc_start: 0.8563 (tpp) cc_final: 0.8352 (tpt) REVERT: D 4938 ASP cc_start: 0.7556 (m-30) cc_final: 0.7345 (m-30) REVERT: D 4967 TYR cc_start: 0.6479 (t80) cc_final: 0.6249 (t80) REVERT: J 4220 ASP cc_start: 0.7630 (m-30) cc_final: 0.7427 (m-30) REVERT: J 4818 MET cc_start: 0.7374 (mmt) cc_final: 0.6845 (ttt) outliers start: 50 outliers final: 29 residues processed: 383 average time/residue: 0.1059 time to fit residues: 60.6961 Evaluate side-chains 363 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 330 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4740 LEU Chi-restraints excluded: chain G residue 4779 LYS Chi-restraints excluded: chain G residue 4797 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4221 VAL Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4707 ASN Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4828 SER Chi-restraints excluded: chain J residue 4836 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4714 ASN A4857 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144556 restraints weight = 17301.477| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.32 r_work: 0.3495 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14070 Z= 0.254 Angle : 0.614 7.539 19128 Z= 0.337 Chirality : 0.041 0.146 2174 Planarity : 0.005 0.063 2340 Dihedral : 8.157 75.791 2028 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.61 % Allowed : 22.97 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1721 helix: 1.25 (0.14), residues: 1206 sheet: 0.09 (0.87), residues: 40 loop : -1.82 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D4734 TYR 0.014 0.002 TYR A4580 PHE 0.026 0.002 PHE G4217 TRP 0.013 0.002 TRP G4778 HIS 0.005 0.002 HIS D4886 Details of bonding type rmsd covalent geometry : bond 0.00549 (14063) covalent geometry : angle 0.61305 (19114) SS BOND : bond 0.00219 ( 7) SS BOND : angle 1.06777 ( 14) hydrogen bonds : bond 0.05788 ( 929) hydrogen bonds : angle 4.48480 ( 2727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 382 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4245 MET cc_start: 0.7955 (mmm) cc_final: 0.7676 (mtt) REVERT: G 4252 SER cc_start: 0.8612 (t) cc_final: 0.8306 (m) REVERT: G 4555 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8674 (tt) REVERT: G 4638 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.5963 (p90) REVERT: A 4215 ARG cc_start: 0.8030 (mmt180) cc_final: 0.7672 (mmt180) REVERT: A 4234 PHE cc_start: 0.8065 (t80) cc_final: 0.7803 (t80) REVERT: A 4553 ASN cc_start: 0.6708 (t0) cc_final: 0.6101 (t0) REVERT: A 4557 ARG cc_start: 0.7621 (ptt90) cc_final: 0.7265 (ptt90) REVERT: A 4571 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: A 4679 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6751 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7668 (t-100) cc_final: 0.7396 (t-100) REVERT: A 4728 HIS cc_start: 0.7866 (m90) cc_final: 0.7665 (m-70) REVERT: A 4796 MET cc_start: 0.7944 (tpt) cc_final: 0.7515 (ttt) REVERT: A 4873 ASP cc_start: 0.8553 (t0) cc_final: 0.8271 (t0) REVERT: A 4877 ASP cc_start: 0.8023 (m-30) cc_final: 0.7681 (t0) REVERT: A 4949 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7845 (mm110) REVERT: A 4959 PHE cc_start: 0.8932 (t80) cc_final: 0.8625 (t80) REVERT: D 4242 ILE cc_start: 0.8960 (mt) cc_final: 0.8729 (mp) REVERT: D 4564 PHE cc_start: 0.8701 (t80) cc_final: 0.8489 (t80) REVERT: D 4676 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: D 4682 GLU cc_start: 0.7819 (pt0) cc_final: 0.7507 (pt0) REVERT: D 4808 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7942 (t80) REVERT: D 4839 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: D 4859 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.7648 (p90) REVERT: D 4873 ASP cc_start: 0.8204 (t0) cc_final: 0.7971 (t0) REVERT: D 4938 ASP cc_start: 0.7854 (m-30) cc_final: 0.7646 (m-30) REVERT: J 4220 ASP cc_start: 0.8006 (m-30) cc_final: 0.7649 (m-30) REVERT: J 4242 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8392 (mt) REVERT: J 4575 PHE cc_start: 0.8355 (t80) cc_final: 0.8134 (t80) REVERT: J 4792 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7971 (mm) REVERT: J 4796 MET cc_start: 0.7949 (tpt) cc_final: 0.7411 (tpt) REVERT: J 4803 HIS cc_start: 0.8044 (m-70) cc_final: 0.7837 (m90) REVERT: J 4818 MET cc_start: 0.8163 (mmt) cc_final: 0.7710 (ttt) outliers start: 74 outliers final: 45 residues processed: 435 average time/residue: 0.0983 time to fit residues: 64.6992 Evaluate side-chains 412 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4697 VAL Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4771 ILE Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4831 THR Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4726 ASP Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4573 ILE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4828 SER Chi-restraints excluded: chain J residue 4853 VAL Chi-restraints excluded: chain J residue 4901 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4574 ASN ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147506 restraints weight = 17177.127| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.15 r_work: 0.3546 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14070 Z= 0.143 Angle : 0.500 9.093 19128 Z= 0.272 Chirality : 0.036 0.122 2174 Planarity : 0.004 0.058 2340 Dihedral : 7.719 72.747 2028 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.93 % Allowed : 25.02 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1721 helix: 1.52 (0.14), residues: 1203 sheet: -0.08 (0.87), residues: 40 loop : -1.87 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J4215 TYR 0.019 0.001 TYR A4630 PHE 0.021 0.001 PHE J4671 TRP 0.014 0.001 TRP J4701 HIS 0.004 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00310 (14063) covalent geometry : angle 0.50000 (19114) SS BOND : bond 0.00126 ( 7) SS BOND : angle 0.75223 ( 14) hydrogen bonds : bond 0.04499 ( 929) hydrogen bonds : angle 4.18471 ( 2727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 367 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8566 (t) cc_final: 0.8285 (m) REVERT: G 4555 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8600 (tt) REVERT: G 4581 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6786 (mmtm) REVERT: G 4674 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 4216 GLN cc_start: 0.8775 (tp40) cc_final: 0.8551 (tp40) REVERT: A 4234 PHE cc_start: 0.7936 (t80) cc_final: 0.7639 (t80) REVERT: A 4571 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: A 4664 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8381 (mt) REVERT: A 4701 TRP cc_start: 0.7586 (t-100) cc_final: 0.7301 (t-100) REVERT: A 4796 MET cc_start: 0.7845 (tpt) cc_final: 0.7452 (ttt) REVERT: A 4877 ASP cc_start: 0.7889 (m-30) cc_final: 0.7505 (t0) REVERT: A 4949 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7677 (tt0) REVERT: A 4959 PHE cc_start: 0.8911 (t80) cc_final: 0.8690 (t80) REVERT: D 4676 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 4808 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7980 (t80) REVERT: D 4859 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7569 (p90) REVERT: D 4899 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: D 4938 ASP cc_start: 0.7876 (m-30) cc_final: 0.7650 (m-30) REVERT: J 4220 ASP cc_start: 0.7971 (m-30) cc_final: 0.7767 (m-30) REVERT: J 4242 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8170 (mt) REVERT: J 4575 PHE cc_start: 0.8329 (t80) cc_final: 0.8081 (t80) REVERT: J 4657 CYS cc_start: 0.8374 (m) cc_final: 0.7993 (m) REVERT: J 4792 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7901 (mm) REVERT: J 4796 MET cc_start: 0.7676 (tpt) cc_final: 0.7100 (tpt) REVERT: J 4803 HIS cc_start: 0.7945 (m-70) cc_final: 0.7693 (m90) REVERT: J 4818 MET cc_start: 0.7929 (mmt) cc_final: 0.7711 (ttt) outliers start: 65 outliers final: 34 residues processed: 410 average time/residue: 0.0997 time to fit residues: 62.0965 Evaluate side-chains 398 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 354 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4581 LYS Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G4949 GLN J4707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147253 restraints weight = 17306.974| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.18 r_work: 0.3510 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14070 Z= 0.152 Angle : 0.512 9.111 19128 Z= 0.276 Chirality : 0.036 0.148 2174 Planarity : 0.004 0.076 2340 Dihedral : 7.483 71.549 2026 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.91 % Allowed : 24.11 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1721 helix: 1.55 (0.14), residues: 1203 sheet: -0.26 (0.88), residues: 40 loop : -1.93 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J4215 TYR 0.019 0.001 TYR A4630 PHE 0.033 0.002 PHE J4671 TRP 0.014 0.001 TRP G4778 HIS 0.003 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00333 (14063) covalent geometry : angle 0.51160 (19114) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.75791 ( 14) hydrogen bonds : bond 0.04494 ( 929) hydrogen bonds : angle 4.16423 ( 2727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 358 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8642 (t) cc_final: 0.8341 (m) REVERT: G 4555 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8572 (tt) REVERT: G 4674 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 4216 GLN cc_start: 0.8800 (tp40) cc_final: 0.8535 (tp40) REVERT: A 4234 PHE cc_start: 0.7890 (t80) cc_final: 0.7558 (t80) REVERT: A 4569 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 4571 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: A 4664 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 4679 ARG cc_start: 0.7140 (mmt90) cc_final: 0.6438 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7630 (t-100) cc_final: 0.7341 (t-100) REVERT: A 4777 ILE cc_start: 0.8377 (tt) cc_final: 0.7970 (mp) REVERT: A 4796 MET cc_start: 0.7750 (tpt) cc_final: 0.7362 (ttt) REVERT: A 4877 ASP cc_start: 0.7831 (m-30) cc_final: 0.7236 (t0) REVERT: A 4949 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7819 (mm110) REVERT: A 4954 MET cc_start: 0.7885 (mmp) cc_final: 0.7643 (mtm) REVERT: A 4959 PHE cc_start: 0.8935 (t80) cc_final: 0.8548 (t80) REVERT: D 4649 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8252 (mp) REVERT: D 4658 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8441 (mt) REVERT: D 4663 CYS cc_start: 0.8258 (t) cc_final: 0.7928 (p) REVERT: D 4676 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 4682 GLU cc_start: 0.7660 (pt0) cc_final: 0.7173 (pt0) REVERT: D 4808 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8169 (t80) REVERT: D 4859 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7634 (p90) REVERT: D 4899 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: D 4938 ASP cc_start: 0.7869 (m-30) cc_final: 0.7633 (m-30) REVERT: J 4242 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8158 (mt) REVERT: J 4575 PHE cc_start: 0.8295 (t80) cc_final: 0.8044 (t80) REVERT: J 4657 CYS cc_start: 0.8363 (m) cc_final: 0.7923 (m) REVERT: J 4792 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7890 (mm) REVERT: J 4796 MET cc_start: 0.7676 (tpt) cc_final: 0.7061 (tpt) REVERT: J 4803 HIS cc_start: 0.7990 (m-70) cc_final: 0.7758 (m90) REVERT: J 4818 MET cc_start: 0.8023 (mmt) cc_final: 0.7768 (ttt) REVERT: J 4948 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8161 (tt0) outliers start: 78 outliers final: 48 residues processed: 408 average time/residue: 0.0936 time to fit residues: 59.1435 Evaluate side-chains 407 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 346 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4866 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4716 TRP Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4836 GLN Chi-restraints excluded: chain J residue 4853 VAL Chi-restraints excluded: chain J residue 4948 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G4949 GLN J4707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.163022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145252 restraints weight = 17213.104| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.35 r_work: 0.3506 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14070 Z= 0.161 Angle : 0.518 10.085 19128 Z= 0.281 Chirality : 0.037 0.180 2174 Planarity : 0.004 0.075 2340 Dihedral : 7.384 70.991 2026 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.07 % Allowed : 24.18 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1721 helix: 1.49 (0.14), residues: 1201 sheet: -0.74 (0.87), residues: 42 loop : -1.90 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J4215 TYR 0.020 0.001 TYR A4630 PHE 0.037 0.002 PHE D4217 TRP 0.014 0.001 TRP J4716 HIS 0.003 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00354 (14063) covalent geometry : angle 0.51812 (19114) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.74711 ( 14) hydrogen bonds : bond 0.04577 ( 929) hydrogen bonds : angle 4.17888 ( 2727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 351 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8765 (t) cc_final: 0.8517 (m) REVERT: G 4555 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8574 (tt) REVERT: G 4676 GLU cc_start: 0.7600 (mp0) cc_final: 0.7385 (mp0) REVERT: A 4216 GLN cc_start: 0.8883 (tp40) cc_final: 0.8550 (tp-100) REVERT: A 4234 PHE cc_start: 0.8111 (t80) cc_final: 0.7791 (t80) REVERT: A 4569 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 4571 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: A 4664 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 4679 ARG cc_start: 0.7156 (mmt90) cc_final: 0.6499 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7774 (t-100) cc_final: 0.7472 (t-100) REVERT: A 4777 ILE cc_start: 0.8448 (tt) cc_final: 0.8048 (mp) REVERT: A 4796 MET cc_start: 0.7823 (tpt) cc_final: 0.7436 (ttt) REVERT: A 4877 ASP cc_start: 0.8021 (m-30) cc_final: 0.7562 (t0) REVERT: A 4949 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7527 (mt0) REVERT: A 4959 PHE cc_start: 0.9006 (t80) cc_final: 0.8565 (t80) REVERT: D 4649 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8385 (mp) REVERT: D 4658 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8600 (mt) REVERT: D 4663 CYS cc_start: 0.8246 (t) cc_final: 0.7956 (p) REVERT: D 4676 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: D 4682 GLU cc_start: 0.7674 (pt0) cc_final: 0.7296 (pt0) REVERT: D 4808 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8360 (t80) REVERT: D 4859 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7754 (p90) REVERT: D 4873 ASP cc_start: 0.7939 (t0) cc_final: 0.7680 (t0) REVERT: D 4899 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: D 4938 ASP cc_start: 0.7949 (m-30) cc_final: 0.7718 (m-30) REVERT: J 4242 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mt) REVERT: J 4555 LEU cc_start: 0.7706 (mp) cc_final: 0.7432 (mp) REVERT: J 4657 CYS cc_start: 0.8465 (m) cc_final: 0.8085 (m) REVERT: J 4792 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7908 (mm) REVERT: J 4796 MET cc_start: 0.7914 (tpt) cc_final: 0.7334 (tpt) REVERT: J 4803 HIS cc_start: 0.8155 (m-70) cc_final: 0.7955 (m90) REVERT: J 4818 MET cc_start: 0.8155 (mmt) cc_final: 0.7833 (ttt) outliers start: 80 outliers final: 50 residues processed: 402 average time/residue: 0.0931 time to fit residues: 58.0763 Evaluate side-chains 398 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain G residue 4236 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4583 SER Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4716 TRP Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4829 SER Chi-restraints excluded: chain G residue 4866 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4836 GLN Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J4707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148114 restraints weight = 17422.093| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.32 r_work: 0.3547 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14070 Z= 0.117 Angle : 0.488 11.729 19128 Z= 0.263 Chirality : 0.035 0.172 2174 Planarity : 0.004 0.060 2340 Dihedral : 7.200 69.069 2026 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.46 % Allowed : 24.64 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1721 helix: 1.67 (0.15), residues: 1203 sheet: -1.21 (0.84), residues: 44 loop : -1.77 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J4215 TYR 0.019 0.001 TYR A4630 PHE 0.032 0.001 PHE D4217 TRP 0.012 0.001 TRP J4716 HIS 0.003 0.001 HIS G4812 Details of bonding type rmsd covalent geometry : bond 0.00251 (14063) covalent geometry : angle 0.48833 (19114) SS BOND : bond 0.00084 ( 7) SS BOND : angle 0.58727 ( 14) hydrogen bonds : bond 0.03970 ( 929) hydrogen bonds : angle 4.03154 ( 2727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4252 SER cc_start: 0.8639 (t) cc_final: 0.8405 (m) REVERT: G 4555 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8516 (tt) REVERT: G 4676 GLU cc_start: 0.7584 (mp0) cc_final: 0.7327 (mp0) REVERT: G 4690 GLU cc_start: 0.7463 (pm20) cc_final: 0.7225 (pm20) REVERT: A 4216 GLN cc_start: 0.8879 (tp40) cc_final: 0.8638 (tp40) REVERT: A 4234 PHE cc_start: 0.8075 (t80) cc_final: 0.7742 (t80) REVERT: A 4569 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 4571 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: A 4664 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 4679 ARG cc_start: 0.7090 (mmt90) cc_final: 0.6442 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7728 (t-100) cc_final: 0.7367 (t-100) REVERT: A 4777 ILE cc_start: 0.8389 (tt) cc_final: 0.7979 (mp) REVERT: A 4796 MET cc_start: 0.7788 (tpt) cc_final: 0.7375 (ttt) REVERT: A 4877 ASP cc_start: 0.7931 (m-30) cc_final: 0.7457 (t0) REVERT: A 4949 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7526 (mt0) REVERT: A 4959 PHE cc_start: 0.8977 (t80) cc_final: 0.8606 (t80) REVERT: D 4649 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8336 (mp) REVERT: D 4658 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8606 (mt) REVERT: D 4663 CYS cc_start: 0.8036 (t) cc_final: 0.7790 (p) REVERT: D 4676 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: D 4682 GLU cc_start: 0.7605 (pt0) cc_final: 0.7279 (pt0) REVERT: D 4700 GLN cc_start: 0.7670 (mp10) cc_final: 0.7150 (mp10) REVERT: D 4808 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8301 (t80) REVERT: D 4859 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7703 (p90) REVERT: D 4899 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: D 4938 ASP cc_start: 0.7969 (m-30) cc_final: 0.7741 (m-30) REVERT: D 4967 TYR cc_start: 0.6395 (t80) cc_final: 0.6118 (t80) REVERT: J 4242 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8181 (mt) REVERT: J 4792 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7926 (mm) REVERT: J 4796 MET cc_start: 0.7771 (tpt) cc_final: 0.7197 (tpt) REVERT: J 4818 MET cc_start: 0.8076 (mmt) cc_final: 0.7790 (ttt) outliers start: 72 outliers final: 47 residues processed: 398 average time/residue: 0.0957 time to fit residues: 59.3472 Evaluate side-chains 409 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4236 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4583 SER Chi-restraints excluded: chain G residue 4638 TYR Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4716 TRP Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4799 SER Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4807 PHE Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4707 ASN Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 150 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4216 GLN J4707 ASN J4803 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144332 restraints weight = 17246.473| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.27 r_work: 0.3503 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14070 Z= 0.185 Angle : 0.558 13.778 19128 Z= 0.298 Chirality : 0.038 0.208 2174 Planarity : 0.004 0.064 2340 Dihedral : 7.323 67.907 2026 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.38 % Allowed : 24.11 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1721 helix: 1.48 (0.14), residues: 1201 sheet: -1.15 (0.84), residues: 42 loop : -1.92 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J4215 TYR 0.021 0.001 TYR A4630 PHE 0.027 0.002 PHE G4217 TRP 0.023 0.002 TRP J4701 HIS 0.008 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00405 (14063) covalent geometry : angle 0.55756 (19114) SS BOND : bond 0.00140 ( 7) SS BOND : angle 0.75783 ( 14) hydrogen bonds : bond 0.04749 ( 929) hydrogen bonds : angle 4.21747 ( 2727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4239 GLU cc_start: 0.7544 (pt0) cc_final: 0.7208 (pt0) REVERT: G 4252 SER cc_start: 0.8748 (t) cc_final: 0.8547 (m) REVERT: G 4555 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8622 (tt) REVERT: G 4672 LYS cc_start: 0.8518 (ttmt) cc_final: 0.7654 (ttmt) REVERT: G 4676 GLU cc_start: 0.7613 (mp0) cc_final: 0.7344 (mp0) REVERT: G 4743 MET cc_start: 0.7729 (mmt) cc_final: 0.7342 (mtt) REVERT: A 4216 GLN cc_start: 0.8870 (tp40) cc_final: 0.8627 (tp40) REVERT: A 4234 PHE cc_start: 0.8080 (t80) cc_final: 0.7736 (t80) REVERT: A 4571 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: A 4664 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 4679 ARG cc_start: 0.7190 (mmt90) cc_final: 0.6513 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7783 (t-100) cc_final: 0.7526 (t-100) REVERT: A 4796 MET cc_start: 0.7865 (tpt) cc_final: 0.7471 (ttt) REVERT: A 4877 ASP cc_start: 0.8040 (m-30) cc_final: 0.7591 (t0) REVERT: A 4949 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7890 (mm110) REVERT: A 4959 PHE cc_start: 0.9063 (t80) cc_final: 0.8569 (t80) REVERT: D 4233 LEU cc_start: 0.8804 (mt) cc_final: 0.8574 (mt) REVERT: D 4242 ILE cc_start: 0.8837 (mt) cc_final: 0.8616 (mp) REVERT: D 4649 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 4658 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (mt) REVERT: D 4676 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: D 4682 GLU cc_start: 0.7642 (pt0) cc_final: 0.7340 (pt0) REVERT: D 4808 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8365 (t80) REVERT: D 4859 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7786 (p90) REVERT: D 4873 ASP cc_start: 0.7902 (t0) cc_final: 0.7680 (t0) REVERT: D 4899 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: D 4938 ASP cc_start: 0.7992 (m-30) cc_final: 0.7777 (m-30) REVERT: D 4967 TYR cc_start: 0.6485 (t80) cc_final: 0.6231 (t80) REVERT: J 4242 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8307 (mt) REVERT: J 4555 LEU cc_start: 0.7786 (mp) cc_final: 0.7525 (mp) REVERT: J 4657 CYS cc_start: 0.8455 (m) cc_final: 0.8026 (m) REVERT: J 4792 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7910 (mm) REVERT: J 4796 MET cc_start: 0.7874 (tpt) cc_final: 0.7328 (tpt) REVERT: J 4818 MET cc_start: 0.8258 (mmt) cc_final: 0.7997 (ttt) outliers start: 71 outliers final: 55 residues processed: 402 average time/residue: 0.0978 time to fit residues: 60.8514 Evaluate side-chains 417 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 351 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4236 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4583 SER Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4705 VAL Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4716 TRP Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4866 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4688 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4799 SER Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4216 GLN Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4687 TYR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4807 PHE Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4707 ASN Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4216 GLN ** J4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J4803 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146701 restraints weight = 17363.757| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.27 r_work: 0.3531 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14070 Z= 0.134 Angle : 0.535 14.926 19128 Z= 0.284 Chirality : 0.036 0.185 2174 Planarity : 0.004 0.064 2340 Dihedral : 7.194 69.261 2024 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.31 % Allowed : 25.09 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1721 helix: 1.57 (0.15), residues: 1201 sheet: -1.28 (0.82), residues: 42 loop : -1.88 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J4215 TYR 0.024 0.001 TYR J4715 PHE 0.041 0.001 PHE D4217 TRP 0.020 0.001 TRP J4701 HIS 0.008 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00293 (14063) covalent geometry : angle 0.53509 (19114) SS BOND : bond 0.00092 ( 7) SS BOND : angle 0.62020 ( 14) hydrogen bonds : bond 0.04262 ( 929) hydrogen bonds : angle 4.13466 ( 2727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 349 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 4239 GLU cc_start: 0.7505 (pt0) cc_final: 0.7193 (pt0) REVERT: G 4252 SER cc_start: 0.8698 (t) cc_final: 0.8484 (m) REVERT: G 4555 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8580 (tt) REVERT: G 4672 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7598 (ttmt) REVERT: G 4674 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7828 (mt-10) REVERT: G 4676 GLU cc_start: 0.7543 (mp0) cc_final: 0.7282 (mp0) REVERT: G 4743 MET cc_start: 0.7710 (mmt) cc_final: 0.7282 (mtt) REVERT: G 4824 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7497 (ttm110) REVERT: A 4216 GLN cc_start: 0.8877 (tp40) cc_final: 0.8617 (tp40) REVERT: A 4234 PHE cc_start: 0.8059 (t80) cc_final: 0.7717 (t80) REVERT: A 4569 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8368 (mp) REVERT: A 4571 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 4664 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8398 (mt) REVERT: A 4679 ARG cc_start: 0.7148 (mmt90) cc_final: 0.6497 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7790 (t-100) cc_final: 0.7492 (t-100) REVERT: A 4796 MET cc_start: 0.7849 (tpt) cc_final: 0.7447 (ttt) REVERT: A 4877 ASP cc_start: 0.8022 (m-30) cc_final: 0.7522 (t0) REVERT: A 4949 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7542 (mt0) REVERT: A 4959 PHE cc_start: 0.9040 (t80) cc_final: 0.8623 (t80) REVERT: D 4233 LEU cc_start: 0.8775 (mt) cc_final: 0.8569 (mt) REVERT: D 4242 ILE cc_start: 0.8821 (mt) cc_final: 0.8590 (mp) REVERT: D 4649 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 4658 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8681 (mt) REVERT: D 4682 GLU cc_start: 0.7631 (pt0) cc_final: 0.7339 (pt0) REVERT: D 4700 GLN cc_start: 0.7694 (mp10) cc_final: 0.7207 (mp10) REVERT: D 4808 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8362 (t80) REVERT: D 4859 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7744 (p90) REVERT: D 4873 ASP cc_start: 0.7858 (t0) cc_final: 0.7623 (t0) REVERT: D 4899 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: D 4938 ASP cc_start: 0.8023 (m-30) cc_final: 0.7807 (m-30) REVERT: D 4967 TYR cc_start: 0.6454 (t80) cc_final: 0.6203 (t80) REVERT: J 4220 ASP cc_start: 0.8004 (m-30) cc_final: 0.7677 (m-30) REVERT: J 4242 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8242 (mt) REVERT: J 4555 LEU cc_start: 0.7571 (mp) cc_final: 0.7357 (mp) REVERT: J 4792 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7976 (mm) REVERT: J 4796 MET cc_start: 0.7800 (tpt) cc_final: 0.7211 (tpt) REVERT: J 4818 MET cc_start: 0.8171 (mmt) cc_final: 0.7931 (ttt) REVERT: J 4900 GLU cc_start: 0.8186 (mp0) cc_final: 0.7952 (mp0) outliers start: 70 outliers final: 49 residues processed: 392 average time/residue: 0.0981 time to fit residues: 59.0195 Evaluate side-chains 401 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 341 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain G residue 4236 SER Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4716 TRP Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4827 LEU Chi-restraints excluded: chain G residue 4866 SER Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4573 ILE Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4719 PHE Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4799 SER Chi-restraints excluded: chain A residue 4828 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4216 GLN Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4807 PHE Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4717 ASP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 124 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 160 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4216 GLN ** J4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148795 restraints weight = 17318.715| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.34 r_work: 0.3553 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14070 Z= 0.117 Angle : 0.525 15.084 19128 Z= 0.276 Chirality : 0.035 0.190 2174 Planarity : 0.004 0.065 2340 Dihedral : 7.034 71.683 2024 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.62 % Allowed : 25.63 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1721 helix: 1.69 (0.15), residues: 1199 sheet: -0.96 (0.98), residues: 32 loop : -1.70 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J4215 TYR 0.020 0.001 TYR A4630 PHE 0.031 0.001 PHE G4217 TRP 0.015 0.001 TRP J4701 HIS 0.007 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00251 (14063) covalent geometry : angle 0.52473 (19114) SS BOND : bond 0.00066 ( 7) SS BOND : angle 0.54738 ( 14) hydrogen bonds : bond 0.03928 ( 929) hydrogen bonds : angle 4.04127 ( 2727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3442 Ramachandran restraints generated. 1721 Oldfield, 0 Emsley, 1721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5792 (mtt180) REVERT: G 4239 GLU cc_start: 0.7491 (pt0) cc_final: 0.7164 (pt0) REVERT: G 4252 SER cc_start: 0.8620 (t) cc_final: 0.8382 (m) REVERT: G 4555 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8572 (tt) REVERT: G 4672 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7597 (ttmt) REVERT: G 4674 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7829 (mt-10) REVERT: G 4676 GLU cc_start: 0.7570 (mp0) cc_final: 0.7348 (mp0) REVERT: G 4743 MET cc_start: 0.7688 (mmt) cc_final: 0.7241 (mtt) REVERT: G 4821 LYS cc_start: 0.7882 (tptt) cc_final: 0.7535 (tppt) REVERT: G 4824 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7533 (ttm110) REVERT: A 4216 GLN cc_start: 0.8869 (tp40) cc_final: 0.8604 (tp40) REVERT: A 4234 PHE cc_start: 0.8035 (t80) cc_final: 0.7661 (t80) REVERT: A 4569 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 4664 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 4679 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6479 (mmt-90) REVERT: A 4701 TRP cc_start: 0.7763 (t-100) cc_final: 0.7440 (t-100) REVERT: A 4796 MET cc_start: 0.7832 (tpt) cc_final: 0.7407 (ttt) REVERT: A 4877 ASP cc_start: 0.8013 (m-30) cc_final: 0.7491 (t0) REVERT: A 4949 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7484 (mt0) REVERT: A 4959 PHE cc_start: 0.9020 (t80) cc_final: 0.8603 (t80) REVERT: D 4242 ILE cc_start: 0.8770 (mt) cc_final: 0.8532 (mp) REVERT: D 4649 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8430 (mp) REVERT: D 4658 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8631 (mt) REVERT: D 4682 GLU cc_start: 0.7590 (pt0) cc_final: 0.7322 (pt0) REVERT: D 4700 GLN cc_start: 0.7660 (mp10) cc_final: 0.7367 (mp10) REVERT: D 4808 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8331 (t80) REVERT: D 4859 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7649 (p90) REVERT: D 4899 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: J 4220 ASP cc_start: 0.8006 (m-30) cc_final: 0.7684 (m-30) REVERT: J 4242 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (mt) REVERT: J 4555 LEU cc_start: 0.7410 (mp) cc_final: 0.7182 (mp) REVERT: J 4792 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7957 (mm) REVERT: J 4796 MET cc_start: 0.7788 (tpt) cc_final: 0.7169 (tpt) REVERT: J 4818 MET cc_start: 0.8115 (mmt) cc_final: 0.7868 (ttt) outliers start: 61 outliers final: 45 residues processed: 379 average time/residue: 0.1019 time to fit residues: 58.7575 Evaluate side-chains 387 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain G residue 4236 SER Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4339 VAL Chi-restraints excluded: chain G residue 4555 LEU Chi-restraints excluded: chain G residue 4558 ASN Chi-restraints excluded: chain G residue 4664 LEU Chi-restraints excluded: chain G residue 4713 SER Chi-restraints excluded: chain G residue 4716 TRP Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4866 SER Chi-restraints excluded: chain G residue 4881 THR Chi-restraints excluded: chain G residue 4968 PHE Chi-restraints excluded: chain A residue 4250 GLN Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4664 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4799 SER Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4649 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4807 PHE Chi-restraints excluded: chain D residue 4808 PHE Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain D residue 4899 ASP Chi-restraints excluded: chain D residue 4963 ILE Chi-restraints excluded: chain J residue 4242 ILE Chi-restraints excluded: chain J residue 4558 ASN Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4628 VAL Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4662 ASN Chi-restraints excluded: chain J residue 4664 LEU Chi-restraints excluded: chain J residue 4666 VAL Chi-restraints excluded: chain J residue 4682 GLU Chi-restraints excluded: chain J residue 4683 PHE Chi-restraints excluded: chain J residue 4688 ILE Chi-restraints excluded: chain J residue 4704 LEU Chi-restraints excluded: chain J residue 4716 TRP Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4853 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4691 GLN ** G4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4946 GLN J4707 ASN ** J4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144843 restraints weight = 17321.419| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.15 r_work: 0.3488 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14070 Z= 0.189 Angle : 0.582 16.927 19128 Z= 0.307 Chirality : 0.039 0.157 2174 Planarity : 0.004 0.069 2340 Dihedral : 7.142 71.231 2023 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.08 % Allowed : 25.70 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1721 helix: 1.49 (0.15), residues: 1198 sheet: -1.50 (0.81), residues: 42 loop : -1.87 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J4215 TYR 0.020 0.001 TYR A4630 PHE 0.027 0.002 PHE J4575 TRP 0.022 0.002 TRP J4701 HIS 0.009 0.001 HIS G4728 Details of bonding type rmsd covalent geometry : bond 0.00413 (14063) covalent geometry : angle 0.58201 (19114) SS BOND : bond 0.00149 ( 7) SS BOND : angle 0.73607 ( 14) hydrogen bonds : bond 0.04770 ( 929) hydrogen bonds : angle 4.28087 ( 2727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.25 seconds wall clock time: 69 minutes 59.14 seconds (4199.14 seconds total)